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Yorodumi- PDB-4nl1: Crystal structure of B. anthracis DHPS with compound 11: (E)-N-[4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nl1 | ||||||
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Title | Crystal structure of B. anthracis DHPS with compound 11: (E)-N-[4-(trifluoromethyl)benzyl]-1-[4-(trifluoromethyl)phenyl]methanimine | ||||||
Components | Dihydropteroate Synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TIM Barrel / TIM barel / Transferase / Pterin / pABA / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hammoudeh, D.I. / White, S.W. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase. Authors: Hammoudeh, D.I. / Date, M. / Yun, M.K. / Zhang, W. / Boyd, V.A. / Viacava Follis, A. / Griffith, E. / Lee, R.E. / Bashford, D. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nl1.cif.gz | 219.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nl1.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nl1_validation.pdf.gz | 970.4 KB | Display | wwPDB validaton report |
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Full document | 4nl1_full_validation.pdf.gz | 976.4 KB | Display | |
Data in XML | 4nl1_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4nl1_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/4nl1 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/4nl1 | HTTPS FTP |
-Related structure data
Related structure data | 4nhvC 4nilC 4nirC 1twsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32883.734 Da / Num. of mol.: 2 / Fragment: UNP residues 5-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A2012 / Gene: folP, BAS0071, BA_0071, GBAA_0071 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VW8, dihydropteroate synthase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Lithium sulfate, Bis-Tris propane, pH 9.0, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2012 / Details: Rosenbaum-Rock double-crystal monochrometer | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→30 Å / Num. obs: 31293 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.174 / Χ2: 0.995 / Net I/σ(I): 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TWS Resolution: 2.3→29.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.3059 / WRfactor Rwork: 0.2383 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7686 / SU B: 15.52 / SU ML: 0.167 / SU R Cruickshank DPI: 0.294 / SU Rfree: 0.2333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.76 Å2 / Biso mean: 64.7842 Å2 / Biso min: 43.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.361 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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